Human Gene KRIT1 (uc003ulu.1)
  Description: Homo sapiens KRIT1, ankyrin repeat containing (KRIT1), transcript variant 1, mRNA.
RefSeq Summary (NM_194456): This gene encodes a protein containing four ankyrin repeats, a band 4.1/ezrin/radixin/moesin (FERM) domain, and multiple NPXY sequences. The encoded protein is localized in the nucleus and cytoplasm. It binds to integrin cytoplasmic domain-associated protein-1 alpha (ICAP1alpha), and plays a critical role in beta1-integrin-mediated cell proliferation. It associates with junction proteins and RAS-related protein 1A (Rap1A), which requires the encoded protein for maintaining the integrity of endothelial junctions. It is also a microtubule-associated protein and may play a role in microtubule targeting. Mutations in this gene result in cerebral cavernous malformations. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009].
Transcript (Including UTRs)
   Position: hg19 chr7:91,828,283-91,875,414 Size: 47,132 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr7:91,830,050-91,871,449 Size: 41,400 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:91,828,283-91,875,414)mRNA (may differ from genome)Protein (736 aa)
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H-INVHGNCLynxMalacardsMGIneXtProt
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KRIT1_HUMAN
DESCRIPTION: RecName: Full=Krev interaction trapped protein 1; Short=Krev interaction trapped 1; AltName: Full=Cerebral cavernous malformations 1 protein;
FUNCTION: Component of the CCM signaling pathway which is a crucial regulator of heart and vessel formation and integrity (By similarity). Negative regulator of angiogenesis. Inhibits endothelial proliferation, apoptosis, migration, lumen formation and sprouting angiogenesis in primary endothelial cells. Promotes AKT phosphorylation in a NOTCH-dependent and independent manner, and inhibits EKR1/2 phosphorylation indirectly through activation of the DELTA-NOTCH cascade. Acts in concert with CDH5 to establish and maintain correct endothelial cell polarity and vascular lumen and these effects are mediated by recruitment and activation of the Par polarity complex and RAP1B. Required for the localization of phosphorylated PRKCZ, PARD3, TIAM1 and RAP1B to the cell junction, and cell junction stabilization. Plays an important role in the maintenance of the intracellular reactive oxygen species (ROS) homeostasis to prevent oxidative cellular damage. Regulates the homeostasis of intracellular ROS through an antioxidant pathway involving FOXO1 and SOD2. Facilitates the down-regulation of cyclin-D1 (CCND1) levels required for cell transition from proliferative growth to quiescence by preventing the accumulation of intracellular ROS through the modulation of FOXO1 and SOD2 levels.
SUBUNIT: Interacts with RAP1A. Interacts with CDH5. Interacts with HEG1 and CCM2; greatly facilitates CCM2-binding to HEG1 (By similarity). Interacts (via FERM domain) with RAP1B.
INTERACTION: Q9BSQ5:CCM2; NbExp=3; IntAct=EBI-1573121, EBI-1573056;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Cell membrane; Peripheral membrane protein. Cell junction. Note=KRIT1 and CDH5 reciprocally regulate their localization to endothelial cell-cell junctions. Association with RAP1 relocalizes KRIT1 from microtubules to cell junction membranes.
TISSUE SPECIFICITY: Low levels in brain. Very weak expression found in heart and muscle.
DOMAIN: The FERM domain mediates binding to RAP1A and RAP1B.
DISEASE: Defects in KRIT1 are the cause of cerebral cavernous malformations type 1 (CCM1) [MIM:116860]. Cerebral cavernous malformations (CCMs) are congenital vascular anomalies of the central nervous system that can result in hemorrhagic stroke, seizures, recurrent headaches, and focal neurologic deficits. CCMs have an incidence of 0.1%-0.5% in the general population and usually present clinically during the 3rd to 5th decade of life. The lesions are characterized by grossly enlarged blood vessels consisting of a single layer of endothelium and without any intervening neural tissue, ranging in diameter from a few millimeters to several centimeters.
SIMILARITY: Contains 4 ANK repeats.
SIMILARITY: Contains 1 FERM domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/KRIT1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): KRIT1
CDC HuGE Published Literature: KRIT1

-  MalaCards Disease Associations
  MalaCards Gene Search: KRIT1
Diseases sorted by gene-association score: cerebral cavernous malformations-1* (1263), angiokeratoma corporis diffusum with arteriovenous fistulas* (100), familial cerebral cavernous malformation 1* (100), central nervous system hemangioma (20), cavernous hemangioma (18), vascular hemostatic disease (17), hemangioma of liver (16), cerebral cavernous malformations-2 (13), cavernous malformation (12), cerebral cavernous malformations 3 (11), intracranial structure hemangioma (11), brain angioma (11), cerebral angioma (11), hemangioma (11), glomuvenous malformations (9), hemangioma of intra-abdominal structure (9), split-hand/foot malformation 1 with sensorineural hearing loss (8), human venous malformation (7), cell type benign neoplasm (6), klippel-trenaunay-weber syndrome (6), hemidystonia (5), venous malformations, multiple cutaneous and mucosal (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.40 RPKM in Testis
Total median expression: 393.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -248.74784-0.317 Picture PostScript Text
3' UTR -423.951767-0.240 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom
IPR019749 - Band_41_domain
IPR014352 - FERM/acyl-CoA-bd_prot_3-hlx
IPR019748 - FERM_central
IPR000299 - FERM_domain

Pfam Domains:
PF00373 - FERM central domain
PF12796 - Ankyrin repeats (3 copies)
PF13637 - Ankyrin repeats (many copies)
PF13857 - Ankyrin repeats (many copies)
PF16705 - NUDIX, or N-terminal NPxY motif-rich, region of KRIT

SCOP Domains:
47031 - Second domain of FERM
48403 - Ankyrin repeat

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3U7D - X-ray MuPIT 4DXA - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00522
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0008017 microtubule binding
GO:0030695 GTPase regulator activity
GO:0044877 macromolecular complex binding

Biological Process:
GO:0001525 angiogenesis
GO:0001937 negative regulation of endothelial cell proliferation
GO:0007264 small GTPase mediated signal transduction
GO:0010596 negative regulation of endothelial cell migration
GO:0016525 negative regulation of angiogenesis
GO:0032092 positive regulation of protein binding
GO:0045454 cell redox homeostasis
GO:0050790 regulation of catalytic activity
GO:2000114 regulation of establishment of cell polarity
GO:2000352 negative regulation of endothelial cell apoptotic process

Cellular Component:
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0030054 cell junction
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  KJ890841 - Synthetic construct Homo sapiens clone ccsbBroadEn_00235 KRIT1 gene, encodes complete protein.
KR712064 - Synthetic construct Homo sapiens clone CCSBHm_00035268 KRIT1 (KRIT1) mRNA, encodes complete protein.
AF388384 - Homo sapiens KRIT1 isoform (CCM1) mRNA, complete cds.
BX648659 - Homo sapiens mRNA; cDNA DKFZp686K2438 (from clone DKFZp686K2438).
JD054228 - Sequence 35252 from Patent EP1572962.
AL049325 - Homo sapiens mRNA; cDNA DKFZp564D036 (from clone DKFZp564D036).
AK056537 - Homo sapiens cDNA FLJ31975 fis, clone NT2RP7008190, highly similar to Krev interaction trapped protein 1.
AK226131 - Homo sapiens mRNA for krev interaction trapped 1 isoform 1 variant, clone: fh02688.
U90268 - Human Krit1 mRNA, complete cds.
BC094684 - Homo sapiens KRIT1, ankyrin repeat containing, mRNA (cDNA clone MGC:102819 IMAGE:6174749), complete cds.
AF296765 - Homo sapiens ankyrin repeat-containing protein (CCM1) mRNA, complete cds.
AF310133 - Homo sapiens krev interaction trapped 1 mRNA, complete cds.
AY380057 - Homo sapiens Krev interaction trapped 1 variant (CCM1) mRNA, complete cds.
AY380058 - Homo sapiens truncated Krev interaction trapped 1 variant Q201X (CCM1) mRNA, complete cds.
AY380059 - Homo sapiens truncated Krev interaction trapped 1 variant 1254delA (CCM1) mRNA, complete cds.
AY380060 - Homo sapiens truncated Krev interaction trapped 1 variant 1681delTA (CCM1) mRNA, complete cds.
BC098442 - Homo sapiens KRIT1, ankyrin repeat containing, mRNA (cDNA clone MGC:104877 IMAGE:5922988), complete cds.
AK055305 - Homo sapiens cDNA FLJ30743 fis, clone FEBRA2000377, highly similar to Krev interaction trapped protein 1.
JD100608 - Sequence 81632 from Patent EP1572962.
JD534385 - Sequence 515409 from Patent EP1572962.
JD292362 - Sequence 273386 from Patent EP1572962.
JD183813 - Sequence 164837 from Patent EP1572962.
JD361156 - Sequence 342180 from Patent EP1572962.
JD344033 - Sequence 325057 from Patent EP1572962.
JD481636 - Sequence 462660 from Patent EP1572962.
JD542639 - Sequence 523663 from Patent EP1572962.
JD212550 - Sequence 193574 from Patent EP1572962.
JD542638 - Sequence 523662 from Patent EP1572962.
JD497709 - Sequence 478733 from Patent EP1572962.
AY993944 - Homo sapiens truncated Krev interaction trapped 1 (KRIT1) mRNA, complete cds.
AB590723 - Synthetic construct DNA, clone: pFN21AE2073, Homo sapiens KRIT1 gene for KRIT1, ankyrin repeat containing, without stop codon, in Flexi system.
DQ591856 - Homo sapiens piRNA piR-58968, complete sequence.
AJ294850 - Homo sapiens partial mRNA for KRIT1 (CCM1 gene).
JD090778 - Sequence 71802 from Patent EP1572962.
JD359454 - Sequence 340478 from Patent EP1572962.
JD142609 - Sequence 123633 from Patent EP1572962.
JD565628 - Sequence 546652 from Patent EP1572962.
JD138981 - Sequence 120005 from Patent EP1572962.
JD214158 - Sequence 195182 from Patent EP1572962.
LR596209 - Homo sapiens partial mRNA for Krev interaction trapped protein 1 (KRIT1 gene).
LR596210 - Homo sapiens partial mRNA for Krev interaction trapped protein 1 (KRIT1 gene).

-  Other Names for This Gene
  Alternate Gene Symbols: A6NNU0, CCM1, KRIT1_HUMAN, NM_194456, NP_919438, O00522, O43894, Q506L6, Q6U276, Q75N19, Q9H180, Q9H264, Q9HAX5
UCSC ID: uc003ulu.1
RefSeq Accession: NM_194456
Protein: O00522 (aka KRIT1_HUMAN or KRT1_HUMAN)
CCDS: CCDS5624.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene KRIT1:
ccm (Familial Cerebral Cavernous Malformation)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_194456.1
exon count: 20CDS single in 3' UTR: no RNA size: 4762
ORF size: 2211CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4388.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.